HsaINT0038483 @ hg38
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen type XX alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr20:63319487-63320197:+
Coord C1 exon
chr20:63319487-63319596
Coord A exon
chr20:63319597-63320038
Coord C2 exon
chr20:63320039-63320197
Length
442 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCTG
5' ss Score
-0.19
3' ss Seq
CCTCCCGTGCCGTCTCACAGGTG
3' ss Score
10.55
Exon sequences
Seq C1 exon
CCGGGAAGAAGTCCCTGACCTACTTCCACCGTGACCCCAGGGCTGCCTTGCAGGAGGCCACCTTCGACCCGCAGGAAGTGAGGAAGATTTTCTTCGGGAGCTTCCACAAG
Seq A exon
GTCCTGGTGCAGCTCGCGCCCCTCTCCCCCGTTCCCCCAGCTCTGGGGCAGCCCAGCCCCACAGGGACCTGCCGGATGCCAACTCCTCTCCCTAGGAGAGCAGGACCTTCCTTGGGAGGGAACATTGACCTGGGGCTCTGTTCCTCTACCCCAGCTCTTCCATCTTAATTGGAGTTGAAGAGCCTCCCAGCCCATCTCTTTGGGACCCACAGACCCCGGGAGGCTCCTGCAGCAGGTGCCATTTGGTCCATTTTACAGAGGGGAAGCCGAGGCCCAGCAAGGGGGGGTTCTCCCAGGGTCCCCCGAAACCTGAGGTGAGGTCAGGTTCCTGACCCCAGGTCCCAGGGATGGGTGTTACTCCCCAGCCCTGGCCTGGCCTTGGGGGCTCAGGTGGGCACCGGCCCCGCCTGGGCTGTGGAGAACCTCCCGTGCCGTCTCACAG
Seq C2 exon
GTGCACGTGGCTGTGGGCCGCTCCAAGGTCAGGCTCTATGTGGACTGCCGGAAGGTGGCTGAGCGGCCCCTTGGGGAGATGGGCAGCCCACCCGCTGCGGGCTTCGTCACGCTGGGGAGGCTGGCCAAGGCCAGGGGCCCCCGGAGCAGTTCGGCCGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203:ENST00000422202:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.154
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCCCTGACCTACTTCCACC
R:
CTTGGCCAGCCTCCCCAG
Band lengths:
230-672
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development